clusterVisualHeatmap-class {goCluster} | R Documentation

## Class "clusterVisualHeatmap", prepares a goCluster analysis for visualization.

### Description

The class will prepare the `goCluster`-result for visualization.

### Details

The class provides a wrapper around the `prepareHeatmap`-function. Please read the corresponding documentation for further details.

### Slots

`prepared`:
  Object of class `"list"`, matches the "tree" structure of the annotation term selection from the significance analysis. But instead of a single annotation term each node holds a combination of the annotation term, the genes that were responsible for the selection of this annotation term and the expression values of these genes.

Additional slots are described in the documentation of the `clusterVisual-class` and `clusterModule-class`.

### Extends

Class `"clusterVisual"`, directly. Class `"clusterModule"`, by class `"clusterVisual"`.

### Methods

config
  `signature(object = "clusterVisualHeatmap")`: interactive setup of the class. There are no options that you can set on this class.
setup
  `signature(object = "clusterVisualHeatmap")`: returns the configuration of the object as a list. Since there are no options to this class, this is always an empty list.
setup<-
  `signature(object = "clusterVisualHeatmap")`: non-interactive setup of the class. Not necessary since this class has no options.
execute
  `signature(object = "clusterVisualHeatmap")`: prepares the selected annotation terms for the visualization.
reset
  `signature(object = "clusterVisualHeatmap")`: resets the results of this class so that the analysis can be run again.
display
  `signature(object = "clusterVisualHeatmap")`: generates the actual graphic for this object.
print
  `signature(x = "clusterVisualHeatmap")`: prints generic information about the object.

### Author(s)

Gunnar Wrobel, http://www.gunnarwrobel.de.

### See Also

`prepareHeatmap`, `goCluster-class`, `clusterModule-class`, `clusterVisual-class`

### Examples

    set.seed(1000)

    data(benomylsetupsmall)

    benomylsetupsmall$classvisu <- "clusterVisualHeatmap"

    a <- new("goCluster")

    execute(a) <- benomylsetupsmall

    if(interactive()){
    ## This example can only be run in an interactive mode

    ## This plot shows only four genes since the loaded dataset
    ## has been reduced to only 100 genes. Try the same with
    ## the full dataset
    display(a, selection = "GO:0003735")
    }

[Package goCluster version 1.0.3 Index]